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European Journal of Human Genetics: EJHG

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https://www.readbyqxmd.com/read/28422133/gene-set-analysis-shows-association-between-fmrp-targets-and-autism-spectrum-disorder
#1
Arija Jansen, Gwen C Dieleman, August B Smit, Matthijs Verhage, Frank C Verhulst, Tinca J C Polderman, Danielle Posthuma
Autism spectrum disorder (ASD) is a heterogeneous group of disorders characterized by problems with social interaction, communication, and repetitive and restricted behavior. Despite its high heritability and the substantial progress made in elucidating genetic associations, the corresponding biological mechanisms are largely unknown. Our objective is to investigate the contribution of common genetic variation to biological pathways functionally involved in ASD. We conducted gene-set analyses to identify ASD-associated functional biological pathways using the statistical tools MAGMA and INRICH...
April 19, 2017: European Journal of Human Genetics: EJHG
https://www.readbyqxmd.com/read/28422132/haploinsufficiency-for-ankrd11-flanking-genes-makes-the-difference-between-kbg-and-16q24-3-microdeletion-syndromes-12-new-cases
#2
Francesca Novara, Berardo Rinaldi, Sanjay M Sisodiya, Antonietta Coppola, Sabrina Giglio, Franco Stanzial, Francesco Benedicenti, Alan Donaldson, Joris Andrieux, Rachel Stapleton, Astrid Weber, Paolo Reho, Conny van Ravenswaaij-Arts, Wilhelmina S Kerstjens-Frederikse, Joris Robert Vermeesch, Koenraad Devriendt, Carlos A Bacino, Andrée Delahaye, S M Maas, Achille Iolascon, Orsetta Zuffardi
16q24 deletion involving the ANKRD11 gene, ranging from 137 kb to 2 Mb, have been associated with a microdeletion syndrome characterized by variable cognitive impairment, autism spectrum disorder, facial dysmorphisms with dental anomalies, brain abnormalities essentially affecting the corpus callosum and short stature. On the other hand, patients carrying either deletions encompassing solely ANKRD11 or its loss-of-function variants were reported in association with the KBG syndrome, characterized by a very similar phenotype, including mild-to-moderate intellectual disability, short stature and macrodontia of upper incisors, with inter and intrafamilial variability...
April 19, 2017: European Journal of Human Genetics: EJHG
https://www.readbyqxmd.com/read/28422131/variants-in-cplx1-in-two-families-with-autosomal-recessive-severe-infantile-myoclonic-epilepsy-and-id
#3
Silke Redler, Tim M Strom, Thomas Wieland, Kirsten Cremer, Hartmut Engels, Felix Distelmaier, Jörg Schaper, Alma Küchler, Johannes R Lemke, Stephanie Jeschke, Nicole Schreyer, Heinrich Sticht, Margarete Koch, Hermann-Josef Lüdecke, Dagmar Wieczorek
For a large number of individuals with intellectual disability (ID), the molecular basis of the disorder is still unknown. However, whole-exome sequencing (WES) is providing more and more insights into the genetic landscape of ID. In the present study, we performed trio-based WES in 311 patients with unsolved ID and additional clinical features, and identified homozygous CPLX1 variants in three patients with ID from two unrelated families. All displayed marked developmental delay and migrating myoclonic epilepsy, and one showed a cerebellar cleft in addition...
April 19, 2017: European Journal of Human Genetics: EJHG
https://www.readbyqxmd.com/read/28401901/missing-heritability-is-the-gap-closing-an-analysis-of-32-complex-traits-in-the-lifelines-cohort-study
#4
Ilja M Nolte, Peter J van der Most, Behrooz Z Alizadeh, Paul Iw de Bakker, H Marike Boezen, Marcel Bruinenberg, Lude Franke, Pim van der Harst, Gerjan Navis, Dirkje S Postma, Marianne G Rots, Ronald P Stolk, Morris A Swertz, Bruce Hr Wolffenbuttel, Cisca Wijmenga, Harold Snieder
Despite the recent explosive rise in number of genetic markers for complex disease traits identified in genome-wide association studies, there is still a large gap between the known heritability of these traits and the part explained by these markers. To gauge whether this 'heritability gap' is closing, we first identified genome-wide significant SNPs from the literature and performed replication analyses for 32 highly relevant traits from five broad disease areas in 13 436 subjects of the Lifelines Cohort...
April 12, 2017: European Journal of Human Genetics: EJHG
https://www.readbyqxmd.com/read/28401900/an-efficient-and-flexible-test-for-rare-variant-effects
#5
Shonosuke Sugasawa, Hisashi Noma, Takahiro Otani, Jo Nishino, Shigeyuki Matsui
Since it has been claimed that rare variants with extremely small allele frequency play a crucial role in complex traits, there is great demand for the development of a powerful test for detecting these variants. However, due to the extremely low frequencies of rare variants, common statistical testing methods do not work well, which has motivated recent extensive research on developing an efficient testing procedure for rare variant effects. Many studies have suggested effective testing procedures with reasonably high power under some presumed assumptions of parametric statistical models...
April 12, 2017: European Journal of Human Genetics: EJHG
https://www.readbyqxmd.com/read/28401899/improved-imputation-accuracy-of-rare-and-low-frequency-variants-using-population-specific-high-coverage-wgs-based-imputation-reference-panel
#6
Mario Mitt, Mart Kals, Kalle Pärn, Stacey B Gabriel, Eric S Lander, Aarno Palotie, Samuli Ripatti, Andrew P Morris, Andres Metspalu, Tõnu Esko, Reedik Mägi, Priit Palta
Genetic imputation is a cost-efficient way to improve the power and resolution of genome-wide association (GWA) studies. Current publicly accessible imputation reference panels accurately predict genotypes for common variants with minor allele frequency (MAF)≥5% and low-frequency variants (0.5≤MAF<5%) across diverse populations, but the imputation of rare variation (MAF<0.5%) is still rather limited. In the current study, we evaluate imputation accuracy achieved with reference panels from diverse populations with a population-specific high-coverage (30 × ) whole-genome sequencing (WGS) based reference panel, comprising of 2244 Estonian individuals (0...
April 12, 2017: European Journal of Human Genetics: EJHG
https://www.readbyqxmd.com/read/28401898/a-unique-haplotype-of-rccx-copy-number-variation-from-the-clinics-of-congenital-adrenal-hyperplasia-to-evolutionary-genetics
#7
Márton Doleschall, Andrea Luczay, Klára Koncz, Kinga Hadzsiev, Éva Erhardt, Ágnes Szilágyi, Zoltán Doleschall, Krisztina Németh, Dóra Török, Zoltán Prohászka, Balázs Gereben, György Fekete, Edit Gláz, Péter Igaz, Márta Korbonits, Miklós Tóth, Károly Rácz, Attila Patócs
There is a difficulty in the molecular diagnosis of congenital adrenal hyperplasia (CAH) due to the c.955C>T (p.(Q319*), formerly Q318X, rs7755898) variant of the CYP21A2 gene. Therefore, a systematic assessment of the genetic and evolutionary relationships between c.955C>T, CYP21A2 haplotypes and the RCCX copy number variation (CNV) structures, which harbor CYP21A2, was performed. In total, 389 unrelated Hungarian individuals with European ancestry (164 healthy subjects, 125 patients with non-functioning adrenal incidentaloma and 100 patients with classical CAH) as well as 34 adrenocortical tumor specimens were studied using a set of experimental and bioinformatic methods...
April 12, 2017: European Journal of Human Genetics: EJHG
https://www.readbyqxmd.com/read/28378820/validation-of-copy-number-variation-analysis-for-next-generation-sequencing-diagnostics
#8
Jamie M Ellingford, Christopher Campbell, Stephanie Barton, Sanjeev Bhaskar, Saurabh Gupta, Rachel L Taylor, Panagiotis I Sergouniotis, Bradley Horn, Janine A Lamb, Michel Michaelides, Andrew R Webster, William G Newman, Binay Panda, Simon C Ramsden, Graeme Cm Black
Although a common cause of disease, copy number variants (CNVs) have not routinely been identified from next-generation sequencing (NGS) data in a clinical context. This study aimed to examine the sensitivity and specificity of a widely used software package, ExomeDepth, to identify CNVs from targeted NGS data sets. We benchmarked the accuracy of CNV detection using ExomeDepth v1.1.6 applied to targeted NGS data sets by comparison to CNV events detected through whole-genome sequencing for 25 individuals and determined the sensitivity and specificity of ExomeDepth applied to these targeted NGS data sets to be 100% and 99...
April 5, 2017: European Journal of Human Genetics: EJHG
https://www.readbyqxmd.com/read/28378819/upstream-slc2a1-translation-initiation-causes-glut1-deficiency-syndrome
#9
Michèl A Willemsen, Lisenka Elm Vissers, Marcel M Verbeek, Bregje W van Bon, Sinje Geuer, Christian Gilissen, Joerg Klepper, Michael P Kwint, Wilhelmina G Leen, Maartje Pennings, Ron A Wevers, Joris A Veltman, Erik-Jan Kamsteeg
Glucose transporter type 1 deficiency syndrome (GLUT1DS) is a neurometabolic disorder with a complex phenotypic spectrum but simple biomarkers in cerebrospinal fluid. The disorder is caused by impaired glucose transport into the brain resulting from variants in SCL2A1. In 10% of GLUT1DS patients, a genetic diagnosis can not be made. Using whole-genome sequencing, we identified a de novo 5'-UTR variant in SLC2A1, generating a novel translation initiation codon, severely compromising SLC2A1 function. This finding expands our understanding of the disease mechanisms underlying GLUT1DS and encourages further in-depth analysis of SLC2A1 non-coding regions in patients without variants in the coding region...
April 5, 2017: European Journal of Human Genetics: EJHG
https://www.readbyqxmd.com/read/28378818/development-and-clinical-utility-of-a-novel-diagnostic-nystagmus-gene-panel-using-targeted-next-generation-sequencing
#10
Mervyn G Thomas, Gail DE Maconachie, Viral Sheth, Rebecca J McLean, Irene Gottlob
Infantile nystagmus (IN) is a genetically heterogeneous disorder arising from variants of genes expressed within the developing retina and brain. IN presents a diagnostic challenge and patients often undergo numerous investigations. We aimed to develop and assess the utility of a next-generation sequencing (NGS) panel to enhance the diagnosis of IN. We identified 336 genes associated with IN from the literature and OMIM. NimbleGen Human custom array was used to enrich the target genes and sequencing was performed using HiSeq2000...
April 5, 2017: European Journal of Human Genetics: EJHG
https://www.readbyqxmd.com/read/28378817/severe-neurodegeneration-progressive-cerebral-volume-loss-and-diffuse-hypomyelination-associated-with-a-homozygous-frameshift-mutation-in-cstb
#11
Alan Brien, Christian R Marshall, Susan Blaser, Peter N Ray, Grace Yoon
Mutations of the cystatin B gene (CSTB; OMIM 601145) are known to cause Unverricht-Lundborg disease or progressive myoclonic epilepsy-1A (EPM1A, MIM #254800). Most patients are homozygous for an expanded (>30) dodecamer repeat in the promoter region of CSTB, or are compound heterozygotes for the dodecamer repeat and a point mutation. We report two adolescent sisters born to consanguineous parents of Sri Lankan descent who presented with profound global developmental delay, microcephaly, cortical blindness and axial hypotonia with appendicular hypertonia...
April 5, 2017: European Journal of Human Genetics: EJHG
https://www.readbyqxmd.com/read/28378816/genetic-variants-associated-with-type-2-diabetes-and-adiposity-and-risk-of-intracranial-and-abdominal-aortic-aneurysms
#12
Femke Ng van 't Hof, Julien Vaucher, Michael V Holmes, Arno de Wilde, Annette F Baas, Jan D Blankensteijn, Albert Hofman, Lambertus Alm Kiemeney, Fernando Rivadeneira, André G Uitterlinden, Sita H Vermeulen, Gabriël Je Rinkel, Paul Iw de Bakker, Ynte M Ruigrok
Epidemiological studies show that type 2 diabetes (T2D) is inversely associated with intracranial aneurysms (IA) and abdominal aortic aneurysms (AAA). Although adiposity has not been considered a risk factor for IA, there have been inconsistent reports relating adiposity to AAA risk. We assessed whether these observations have a genetic, causal basis. To this end, we extracted genotypes of validated single-nucleotide polymorphisms associated with T2D (n=65), body mass index (BMI) (n=97) and waist-hip ratio adjusted for BMI (WHRadjBMI) (n=47) from genotype data collected in 717 IA cases and 1988 controls, and in 818 AAA cases and 3004 controls, all of Dutch descent...
April 5, 2017: European Journal of Human Genetics: EJHG
https://www.readbyqxmd.com/read/28327576/genotypic-spectrum-and-phenotype-correlations-of-abca4-associated-disease-in-patients-of-south-asian-descent
#13
Winston Lee, Kaspar Schuerch, Jana Zernant, Frederick T Collison, Srilaxmi Bearelly, Gerald A Fishman, Stephen H Tsang, Janet R Sparrow, Rando Allikmets
Variants in the ABCA4 gene are the most common cause of juvenile-onset blindness affecting close to 1 in 10 000 people worldwide. Disease severity varies largely according to genotype, which can be specific to ethnic and racial groups. Here we investigate the spectrum of ABCA4 variation and its phenotypic expression in 38 patients of South Asian descent, notably from India, Pakistan, Bangladesh and Sri Lanka. Sequencing of all exons and flanking intronic sequences of ABCA4 revealed disease-causing variants in all patients: 3 in 2...
March 22, 2017: European Journal of Human Genetics: EJHG
https://www.readbyqxmd.com/read/28327575/analysis-of-exome-data-for-4293-trios-suggests-gpi-anchor-biogenesis-defects-are-a-rare-cause-of-developmental-disorders
#14
Alistair T Pagnamenta, Yoshiko Murakami, John M Taylor, Consuelo Anzilotti, Malcolm F Howard, Venessa Miller, Diana S Johnson, Shereen Tadros, Sahar Mansour, I Karen Temple, Rachel Firth, Elisabeth Rosser, Rachel E Harrison, Bronwen Kerr, Niko Popitsch, Taroh Kinoshita, Jenny C Taylor, Usha Kini
Over 150 different proteins attach to the plasma membrane using glycosylphosphatidylinositol (GPI) anchors. Mutations in 18 genes that encode components of GPI-anchor biogenesis result in a phenotypic spectrum that includes learning disability, epilepsy, microcephaly, congenital malformations and mild dysmorphic features. To determine the incidence of GPI-anchor defects, we analysed the exome data from 4293 parent-child trios recruited to the Deciphering Developmental Disorders (DDD) study. All probands recruited had a neurodevelopmental disorder...
March 22, 2017: European Journal of Human Genetics: EJHG
https://www.readbyqxmd.com/read/28327574/from-older-to-younger-intergenerational-promotion-of-health-behaviours-in-portuguese-families-affected-by-familial-amyloid-polyneuropathy
#15
Carla Roma Oliveira, Alvaro Mendes, Liliana Sousa
The role of older generations in families with hereditary diseases has been recognised and associated to their function as guardians of the family's medical history. However, research is scarce in examining the roles that older generations play in terms of health promotion and risk management towards younger generations, which is particularly evident with incurable genetically inherited disorders such as familial amyloid polyneuropathy (FAP) ATTR Val30Met. This qualitative exploratory study examines the roles that older generations play towards younger generations, in terms of health promotion and risk management, in families with FAP...
March 22, 2017: European Journal of Human Genetics: EJHG
https://www.readbyqxmd.com/read/28327573/clinical-utility-gene-card-for-fabry-disease-update-2016
#16
Andreas Gal, Michael Beck, Wolfgang Höppner, Dominique P Germain
No abstract text is available yet for this article.
March 22, 2017: European Journal of Human Genetics: EJHG
https://www.readbyqxmd.com/read/28327572/the-role-of-genetic-counsellors-in-genomic-healthcare-in-the-united-kingdom-a-statement-by-the-association-of-genetic-nurses-and-counsellors
#17
Anna Middleton, Peter Marks, Anita Bruce, Liwsi K Protheroe-Davies, Cath King, Oonagh Claber, Catherine Houghton, Claire Giffney, Rhona Macleod, Claire Dolling, Sue Kenwrick, Diana Scotcher, Georgina Hall, Christine Patch, Laura Boyes
In the United Kingdom, genetic counsellors work together with clinical geneticists and clinical scientist colleagues within specialist genetics services, but they also often work in multidisciplinary teams (MDTs) outside of such services. There, they contribute genetic knowledge together with expert understanding of how to communicate genetic information effectively. They can offer education and support to the MDT, while providing management advice for both affected patients and the extended at-risk family members...
March 22, 2017: European Journal of Human Genetics: EJHG
https://www.readbyqxmd.com/read/28327571/insights-from-early-experience-of-a-rare-disease-genomic-medicine-multidisciplinary-team-a-qualitative-study
#18
Elizabeth Ormondroyd, Michael P Mackley, Edward Blair, Jude Craft, Julian C Knight, John Taylor, Jenny C Taylor, Andrew Om Wilkie, Hugh Watkins
Whole-exome/whole-genome sequencing (WES/WGS) has the potential to enhance genetic diagnosis of rare disease, and is increasingly becoming part of routine clinical care in mainstream medicine. Effective translation will require ongoing efforts in a number of areas including: selection of appropriate patients, provision of effective consent, pre- and post-test genetic counselling, improving variant interpretation algorithms and practices, and management of secondary findings including those found incidentally and those actively sought...
March 22, 2017: European Journal of Human Genetics: EJHG
https://www.readbyqxmd.com/read/28295041/exome-sequencing-identifies-primary-carnitine-deficiency-in-a-family-with-cardiomyopathy-and-sudden-death
#19
Najim Lahrouchi, Elisabeth M Lodder, Maria Mansouri, Rafik Tadros, Layla Zniber, Najlae Adadi, Sally-Ann B Clur, Karin Y van Spaendonck-Zwarts, Alex V Postma, Abdelaziz Sefiani, Ilham Ratbi, Connie R Bezzina
Pediatric cardiomyopathy is a rare but severe disease with high morbidity and mortality. The causes are poorly understood and can only be established in one-third of cases. Recent advances in genetic technologies, specifically next-generation sequencing, now allow for the detection of genetic causes of cardiomyopathy in a systematic and unbiased manner. This is particularly important given the large clinical variability among pediatric cardiomyopathy patients and the large number of genes (>100) implicated in the disorder...
March 15, 2017: European Journal of Human Genetics: EJHG
https://www.readbyqxmd.com/read/28295040/personal-utility-in-genomic-testing-a-systematic-literature-review
#20
REVIEW
Jennefer N Kohler, Erin Turbitt, Barbara B Biesecker
Researchers and clinicians refer to outcomes of genomic testing that extend beyond clinical utility as 'personal utility'. No systematic delineation of personal utility exists, making it challenging to appreciate its scope. Identifying empirical elements of personal utility reported in the literature offers an inventory that can be subsequently ranked for its relative value by those who have undergone genomic testing. A systematic review was conducted of the peer-reviewed literature reporting non-health-related outcomes of genomic testing from 1 January 2003 to 5 August 2016...
March 15, 2017: European Journal of Human Genetics: EJHG
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